GLVR - BACSU - GREMLIN Contacts

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GLVR - HTH-type transcriptional regulator GlvR

UniProt:	P54717	Sequences: MQLEELINQHYSKLNDNDFHILKYILNHKHTCYHLGIDALAKACSVSRSSILRLAQKLGFSGYSEFRVFLKWEDQPEEGESMSFEKLLDDIEANLKFLRTKDMTDMCQLIDAADRIFVYGSGNAQKICARDLQRMFIPRHRYLILIEDTNEFNLMRDDFKVNDLFIIISLSGETPELIPQARMLSAKGIPFISITNLKNNVLAQLTPHNLYATSKPVTLSDRTEIVAFAPFFLVGEALFRAYVDYKEAEKNDNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (235)
Sequences:	9233 (6517)
Seq/√Len:	425.1

ECOLI - YFHH MURR HEXR RPIR
BACSU - GLVR YBBH

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_D	162_N	4.630	1.00
193_S	206_T	3.745	1.00
109_L	190_P	3.018	1.00
182_R	205_L	3.011	1.00
173_E	201_V	2.937	1.00
167_I	181_A	2.776	1.00
118_V	129_A	2.637	1.00
11_Y	23_K	2.566	1.00
114_D	160_K	2.460	1.00
106_M	208_H	2.439	1.00
60_F	69_F	2.422	1.00
10_H	13_K	2.419	1.00
106_M	192_I	2.349	1.00
38_D	57_K	2.330	1.00
89_D	93_A	2.261	1.00
185_S	207_P	2.206	1.00
132_L	136_F	2.166	1.00
181_A	191_F	2.149	1.00
28_H	31_T	2.128	1.00
165_F	184_L	2.113	1.00
160_K	163_D	2.036	1.00
183_M	186_A	2.014	1.00
159_F	189_I	2.002	1.00
114_D	163_D	1.948	1.00
221_D	224_E	1.948	1.00
23_K	27_N	1.924	1.00
164_L	192_I	1.902	1.00
118_V	132_L	1.885	1.00
59_G	62_G	1.884	1.00
109_L	208_H	1.865	1.00
24_Y	28_H	1.854	1.00
113_A	164_L	1.836	1.00
181_A	202_L	1.829	1.00
190_P	207_P	1.815	1.00
118_V	166_I	1.781	1.00
88_L	92_E	1.773	1.00
99_R	102_D	1.756	1.00
129_A	168_I	1.743	1.00
107_C	241_A	1.725	1.00
167_I	177_L	1.724	1.00
22_L	54_L	1.720	1.00
169_S	202_L	1.700	1.00
168_I	194_I	1.635	1.00
115_R	142_Y	1.601	1.00
102_D	105_D	1.594	1.00
184_L	189_I	1.545	1.00
18_D	57_K	1.541	1.00
40_L	53_R	1.537	1.00
35_L	43_A	1.534	1.00
193_S	209_N	1.526	1.00
105_D	208_H	1.520	1.00
190_P	208_H	1.520	1.00
55_A	66_F	1.512	1.00
108_Q	245_Y	1.509	1.00
61_S	65_E	1.474	1.00
191_F	206_T	1.455	1.00
65_E	73_E	1.451	1.00
119_Y	165_F	1.430	1.00
193_S	202_L	1.428	1.00
108_Q	112_A	1.400	1.00
40_L	56_Q	1.386	1.00
109_L	164_L	1.380	1.00
63_Y	67_R	1.378	1.00
238_L	242_Y	1.377	1.00
130_R	147_E	1.373	1.00
165_F	189_I	1.371	1.00
21_I	54_L	1.363	1.00
115_R	144_I	1.345	1.00
133_Q	145_L	1.345	1.00
11_Y	19_F	1.339	1.00
68_V	71_K	1.334	1.00
40_L	57_K	1.333	1.00
62_G	65_E	1.319	1.00
203_A	209_N	1.316	1.00
167_I	191_F	1.303	1.00
64_S	67_R	1.262	1.00
62_G	66_F	1.256	1.00
175_P	179_P	1.255	1.00
115_R	163_D	1.252	1.00
19_F	23_K	1.229	1.00
116_I	141_R	1.217	1.00
74_D	82_M	1.196	1.00
69_F	72_W	1.189	1.00
216_P	220_S	1.173	1.00
106_M	109_L	1.171	1.00
75_Q	78_E	1.170	1.00
185_S	205_L	1.166	1.00
179_P	182_R	1.153	1.00
65_E	69_F	1.153	1.00
69_F	73_E	1.138	1.00
60_F	66_F	1.133	1.00
126_K	130_R	1.129	1.00
63_Y	66_F	1.129	1.00
37_I	52_L	1.122	1.00
166_I	194_I	1.118	1.00
94_N	213_T	1.100	1.00
60_F	63_Y	1.099	1.00
31_T	43_A	1.092	1.00
111_D	242_Y	1.091	1.00
127_I	130_R	1.091	1.00
17_N	20_H	1.084	1.00
67_R	71_K	1.074	1.00
65_E	68_V	1.072	1.00
92_E	96_K	1.061	1.00
159_F	163_D	1.058	1.00
153_N	179_P	1.048	1.00
167_I	184_L	1.044	1.00
24_Y	44_C	1.036	1.00
31_T	35_L	1.034	1.00
17_N	50_S	1.032	1.00
110_I	164_L	1.025	1.00
105_D	109_L	1.024	1.00
112_A	190_P	1.012	1.00
84_F	91_I	1.001	1.00
9_Q	13_K	0.995	1.00
163_D	189_I	0.995	1.00
102_D	208_H	0.994	1.00
117_F	163_D	0.988	1.00
118_V	136_F	0.984	1.00
136_F	236_E	0.979	1.00
228_F	231_F	0.966	1.00
14_L	40_L	0.966	1.00
115_R	145_L	0.966	1.00
70_L	73_E	0.951	1.00
217_V	220_S	0.950	1.00
117_F	159_F	0.948	1.00
24_Y	43_A	0.947	1.00
38_D	48_R	0.945	1.00
94_N	212_A	0.944	1.00
93_A	96_K	0.944	1.00
20_H	52_L	0.944	1.00
37_I	41_A	0.941	1.00
35_L	39_A	0.941	1.00
116_I	164_L	0.938	1.00
68_V	72_W	0.937	1.00
203_A	211_Y	0.936	1.00
24_Y	31_T	0.933	1.00
178_I	201_V	0.931	1.00
184_L	191_F	0.927	1.00
133_Q	137_I	0.926	1.00
136_F	239_F	0.925	1.00
132_L	166_I	0.922	1.00
21_I	44_C	0.913	1.00
164_L	190_P	0.907	1.00
24_Y	35_L	0.905	1.00
132_L	235_G	0.900	1.00
195_T	203_A	0.900	1.00
66_F	70_L	0.891	1.00
77_E	81_S	0.888	1.00
123_N	221_D	0.883	1.00
128_C	235_G	0.883	1.00
182_R	186_A	0.875	1.00
33_Y	37_I	0.873	1.00
40_L	51_I	0.867	1.00
10_H	14_L	0.863	1.00
88_L	91_I	0.857	1.00
40_L	63_Y	0.852	1.00
94_N	97_F	0.851	1.00
81_S	95_L	0.849	1.00
55_A	62_G	0.844	1.00
183_M	187_K	0.843	1.00
89_D	92_E	0.843	1.00
133_Q	143_L	0.842	1.00
168_I	232_F	0.840	1.00
101_K	104_T	0.840	1.00
108_Q	111_D	0.836	1.00
52_L	62_G	0.833	1.00
114_D	142_Y	0.832	1.00
131_D	135_M	0.829	1.00
159_F	165_F	0.829	1.00
14_L	56_Q	0.819	1.00
63_Y	73_E	0.819	1.00
11_Y	22_L	0.818	1.00
228_F	232_F	0.815	1.00
113_A	163_D	0.811	1.00
20_H	45_S	0.808	1.00
238_L	241_A	0.806	1.00
178_I	182_R	0.805	1.00
81_S	85_E	0.804	1.00
91_I	230_P	0.792	1.00
107_C	111_D	0.791	1.00
111_D	245_Y	0.786	1.00
39_A	42_K	0.785	1.00
22_L	26_L	0.782	1.00
36_G	39_A	0.782	1.00
169_S	172_G	0.779	1.00
66_F	73_E	0.773	1.00
83_S	87_L	0.765	1.00
49_S	52_L	0.761	1.00
110_I	166_I	0.761	1.00
128_C	168_I	0.761	1.00
105_D	108_Q	0.759	1.00
90_D	227_A	0.758	1.00
112_A	162_N	0.758	1.00
15_N	18_D	0.757	1.00
118_V	133_Q	0.755	1.00
146_I	155_M	0.755	1.00
106_M	210_L	0.755	1.00
198_K	211_Y	0.754	1.00
79_G	83_S	0.748	1.00
138_P	156_R	0.746	1.00
133_Q	144_I	0.744	1.00
48_R	52_L	0.744	1.00
79_G	82_M	0.743	1.00
150_N	176_E	0.743	1.00
208_H	211_Y	0.740	1.00
115_R	160_K	0.739	1.00
25_I	66_F	0.738	1.00
50_S	53_R	0.738	1.00
21_I	50_S	0.735	1.00
93_A	97_F	0.734	1.00
104_T	241_A	0.733	1.00
51_I	73_E	0.731	1.00
17_N	56_Q	0.729	1.00
32_C	70_L	0.728	1.00
98_L	234_V	0.726	1.00
14_L	57_K	0.725	1.00
109_L	112_A	0.724	1.00
141_R	158_D	0.721	1.00
104_T	245_Y	0.719	1.00
62_G	67_R	0.715	1.00
230_P	233_L	0.712	1.00
110_I	113_A	0.706	1.00
168_I	235_G	0.706	1.00
117_F	165_F	0.706	1.00
212_A	231_F	0.706	1.00
166_I	192_I	0.705	1.00
58_L	72_W	0.704	1.00
216_P	223_T	0.701	1.00
102_D	106_M	0.698	1.00
118_V	143_L	0.697	1.00
215_K	218_T	0.696	1.00
130_R	133_Q	0.695	1.00
141_R	156_R	0.691	1.00
15_N	57_K	0.688	1.00
132_L	135_M	0.680	1.00
121_S	174_T	0.678	1.00
201_V	205_L	0.677	1.00
59_G	63_Y	0.675	1.00
77_E	100_T	0.675	1.00
21_I	46_V	0.675	1.00
76_P	85_E	0.673	1.00
97_F	213_T	0.672	1.00
110_I	116_I	0.669	1.00
206_T	209_N	0.668	1.00
33_Y	36_G	0.668	1.00
116_I	166_I	0.664	1.00
147_E	155_M	0.663	0.99
118_V	168_I	0.663	0.99
126_K	145_L	0.662	0.99
215_K	219_L	0.657	0.99
215_K	220_S	0.657	0.99
181_A	205_L	0.645	0.99
101_K	105_D	0.645	0.99
137_I	155_M	0.638	0.99
153_N	183_M	0.637	0.99
36_G	41_A	0.636	0.99
30_H	33_Y	0.632	0.99
171_S	174_T	0.631	0.99
53_R	57_K	0.627	0.99
32_C	35_L	0.626	0.99
193_S	200_N	0.622	0.99
59_G	66_F	0.620	0.99
195_T	209_N	0.620	0.99
218_T	221_D	0.619	0.99
157_D	183_M	0.617	0.99
224_E	227_A	0.616	0.99
107_C	242_Y	0.615	0.99
113_A	190_P	0.614	0.99
107_C	245_Y	0.613	0.99
178_I	202_L	0.611	0.99
156_R	187_K	0.610	0.99
167_I	180_Q	0.608	0.99
25_I	32_C	0.603	0.99
9_Q	12_S	0.600	0.99
85_E	92_E	0.594	0.99
84_F	87_L	0.591	0.99
178_I	205_L	0.590	0.99
64_S	68_V	0.590	0.99
229_A	233_L	0.589	0.99
120_G	124_A	0.589	0.99
167_I	193_S	0.586	0.99
212_A	227_A	0.585	0.99
131_D	228_F	0.584	0.99
162_N	190_P	0.582	0.99
216_P	219_L	0.581	0.99
200_N	203_A	0.580	0.99
78_E	81_S	0.579	0.99
94_N	230_P	0.577	0.99
55_A	60_F	0.575	0.99
136_F	242_Y	0.575	0.99
87_L	91_I	0.574	0.99
241_A	245_Y	0.574	0.99
88_L	95_L	0.573	0.99
195_T	200_N	0.572	0.99
15_N	40_L	0.571	0.99
156_R	183_M	0.570	0.98
179_P	183_M	0.570	0.98
233_L	236_E	0.569	0.98
173_E	196_N	0.567	0.98
21_I	51_I	0.566	0.98
29_K	32_C	0.566	0.98
116_I	136_F	0.565	0.98
14_L	18_D	0.565	0.98
25_I	54_L	0.562	0.98
132_L	232_F	0.562	0.98
39_A	43_A	0.561	0.98
80_E	84_F	0.558	0.98
12_S	19_F	0.557	0.98
210_L	231_F	0.556	0.98
67_R	70_L	0.554	0.98
119_Y	180_Q	0.554	0.98
126_K	147_E	0.554	0.98
126_K	148_D	0.553	0.98
94_N	98_L	0.552	0.98
80_E	100_T	0.550	0.98
181_A	206_T	0.547	0.98
84_F	233_L	0.547	0.98
55_A	69_F	0.544	0.98
18_D	21_I	0.543	0.98
20_H	51_I	0.543	0.98
237_A	240_R	0.541	0.98
161_V	188_G	0.540	0.98
20_H	23_K	0.538	0.98
66_F	69_F	0.538	0.98
53_R	56_Q	0.532	0.98
196_N	212_A	0.532	0.98
60_F	65_E	0.531	0.98
117_F	146_I	0.531	0.98
33_Y	71_K	0.529	0.98
76_P	104_T	0.529	0.98
137_I	143_L	0.529	0.98
119_Y	167_I	0.528	0.98
121_S	176_E	0.526	0.97
35_L	40_L	0.525	0.97
152_F	180_Q	0.525	0.97
135_M	233_L	0.520	0.97
136_F	144_I	0.520	0.97
135_M	236_E	0.516	0.97
128_C	212_A	0.516	0.97
120_G	126_K	0.515	0.97
58_L	62_G	0.514	0.97
94_N	231_F	0.513	0.97
100_T	104_T	0.507	0.97
141_R	242_Y	0.507	0.97
170_L	223_T	0.507	0.97
170_L	212_A	0.506	0.97
29_K	33_Y	0.505	0.97
185_S	191_F	0.502	0.97
106_M	238_L	0.501	0.97
41_A	53_R	0.500	0.97
20_H	48_R	0.500	0.97

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4ivnA	2	0.9882	100	0.138	Contact Map
3shoA	4	0.685	100	0.522	Contact Map
3fxaA	4	0.7244	100	0.532	Contact Map
2xhzA	4	0.6772	99.9	0.535	Contact Map
3etnA	4	0.7087	99.9	0.543	Contact Map
1vimA	4	0.6811	99.9	0.55	Contact Map
1m3sA	4	0.6772	99.9	0.55	Contact Map
1jeoA	4	0.6496	99.9	0.563	Contact Map
2pocA	4	0.6929	99.9	0.579	Contact Map
1x92A	4	0.6654	99.9	0.585	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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